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Detailed information for vg0228810943:

Variant ID: vg0228810943 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 28810943
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.03, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


ACATAAAAAAACAGCTAATAAGCAGCACAAATTGAGTATTCAGGAATCGGTCTGTCTCTATACTCTGTCGAAGCATTATTATACAGTATACTATAAAAAA[T/A]
TTGCCGACAGAATTGCATTAATTCACTTGAAACAAAAAGAAAACAATTGATCGCAATCTTGCATCTAATGCAATCACTTTCTGAAGTACTAATCCATTTT

Reverse complement sequence

AAAATGGATTAGTACTTCAGAAAGTGATTGCATTAGATGCAAGATTGCGATCAATTGTTTTCTTTTTGTTTCAAGTGAATTAATGCAATTCTGTCGGCAA[A/T]
TTTTTTATAGTATACTGTATAATAATGCTTCGACAGAGTATAGAGACAGACCGATTCCTGAATACTCAATTTGTGCTGCTTATTAGCTGTTTTTTTATGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.50% 5.50% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 85.60% 14.40% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 57.70% 42.30% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 66.70% 33.30% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0228810943 T -> A LOC_Os02g47180.1 downstream_gene_variant ; 4951.0bp to feature; MODIFIER silent_mutation Average:75.229; most accessible tissue: Minghui63 flag leaf, score: 91.625 N N N N
vg0228810943 T -> A LOC_Os02g47200.1 downstream_gene_variant ; 1448.0bp to feature; MODIFIER silent_mutation Average:75.229; most accessible tissue: Minghui63 flag leaf, score: 91.625 N N N N
vg0228810943 T -> A LOC_Os02g47210.1 downstream_gene_variant ; 4523.0bp to feature; MODIFIER silent_mutation Average:75.229; most accessible tissue: Minghui63 flag leaf, score: 91.625 N N N N
vg0228810943 T -> A LOC_Os02g47180.2 downstream_gene_variant ; 4951.0bp to feature; MODIFIER silent_mutation Average:75.229; most accessible tissue: Minghui63 flag leaf, score: 91.625 N N N N
vg0228810943 T -> A LOC_Os02g47190.1 intron_variant ; MODIFIER silent_mutation Average:75.229; most accessible tissue: Minghui63 flag leaf, score: 91.625 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0228810943 T A 0.05 -0.01 -0.01 0.0 0.0 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0228810943 NA 1.56E-08 mr1076 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0228810943 NA 6.60E-08 mr1082 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0228810943 NA 4.06E-07 mr1083 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0228810943 NA 7.03E-06 mr1086 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0228810943 NA 2.61E-06 mr1103 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0228810943 NA 4.71E-09 mr1226 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0228810943 NA 4.93E-07 mr1227 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0228810943 NA 1.34E-06 mr1411 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0228810943 NA 4.09E-06 mr1152_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0228810943 NA 5.62E-07 mr1226_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251